1
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Karlov DS, Long SL, Zeng X, Xu F, Lal K, Cao L, Hayoun K, Lin J, Joyce SA, Tikhonova IG. Characterization of the mechanism of bile salt hydrolase substrate specificity by experimental and computational analyses. Structure 2023; 31:629-638.e5. [PMID: 36963397 DOI: 10.1016/j.str.2023.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/02/2023] [Accepted: 02/27/2023] [Indexed: 03/26/2023]
Abstract
Bile salt hydrolases (BSHs) are currently being investigated as target enzymes for metabolic regulators in humans and as growth promoters in farm animals. Understanding structural features underlying substrate specificity is necessary for inhibitor design. Here, we used a multidisciplinary workflow including mass spectrometry, mutagenesis, molecular dynamic simulations, machine learning, and crystallography to demonstrate substrate specificity in Lactobacillus salivarius BSH, the most abundant enzyme in human and farm animal intestines. We show the preference of substrates with a taurine head and a dehydroxylated sterol ring for hydrolysis. A regression model that correlates the relative rates of hydrolysis of various substrates in various enzyme mutants with the residue-substrate interaction energies guided the identification of structural determinants of substrate binding and specificity. In addition, we found T208 from another BSH protomer regulating the hydrolysis. The designed workflow can be used for fast and comprehensive characterization of enzymes with a broad range of substrates.
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Affiliation(s)
- Dmitry S Karlov
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, UK
| | - Sarah L Long
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT20, Ireland; APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Ximin Zeng
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Fuzhou Xu
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA; Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Kanhaya Lal
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, UK
| | - Liu Cao
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Karim Hayoun
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT20, Ireland; APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Jun Lin
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT20, Ireland; APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, UK.
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2
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Proia E, Ragno A, Antonini L, Sabatino M, Mladenovič M, Capobianco R, Ragno R. Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal. J Comput Aided Mol Des 2022; 36:483-505. [PMID: 35716228 PMCID: PMC9206107 DOI: 10.1007/s10822-022-00460-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/28/2022] [Indexed: 11/05/2022]
Abstract
The main protease (Mpro) of SARS-Cov-2 is the essential enzyme for maturation of functional proteins implicated in viral replication and transcription. The peculiarity of its specific cleavage site joint with its high degree of conservation among all coronaviruses promote it as an attractive target to develop broad-spectrum inhibitors, with high selectivity and tolerable safety profile. Herein is reported a combination of three-dimensional quantitative structure-activity relationships (3-D QSAR) and comparative molecular binding energy (COMBINE) analysis to build robust and predictive ligand-based and structure-based statistical models, respectively. Models were trained on experimental binding poses of co-crystallized Mpro-inhibitors and validated on available literature data. By means of deep optimization both models' goodness and robustness reached final statistical values of r2/q2 values of 0.97/0.79 and 0.93/0.79 for the 3-D QSAR and COMBINE approaches respectively, and an overall predictiveness values of 0.68 and 0.57 for the SDEPPRED and AAEP metrics after application to a test set of 60 compounds covered by the training set applicability domain. Despite the different nature (ligand-based and structure-based) of the employed methods, their outcome fully converged. Furthermore, joint ligand- and structure-based structure-activity relationships were found in good agreement with nirmatrelvir chemical features properties, a novel oral Mpro-inhibitor that has recently received U.S. FDA emergency use authorization (EUA) for the oral treatment of mild-to-moderate COVID-19 infected patients. The obtained results will guide future rational design and/or virtual screening campaigns with the aim of discovering new potential anti-coronavirus lead candidates, minimizing both time and financial resources. Moreover, as most of calculation were performed through the well-established web portal 3d-qsar.com the results confirm the portal as a useful tool for drug design.
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Affiliation(s)
- Eleonora Proia
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Alessio Ragno
- Department of Computer, Control and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Rome, Italy
| | - Lorenzo Antonini
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Manuela Sabatino
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Milan Mladenovič
- Department of Chemistry, Faculty of Science, Kragujevac Center for Computational Biochemistry, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000, Kragujevac, Serbia
| | - Roberto Capobianco
- Department of Computer, Control and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Rome, Italy
- Sony AI, Rome, Italy
| | - Rino Ragno
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
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3
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Nunes-Alves A, Ormersbach F, Wade RC. Prediction of the Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis. J Chem Inf Model 2021; 61:3708-3721. [PMID: 34197096 DOI: 10.1021/acs.jcim.1c00639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is growing consensus that the optimization of the kinetic parameters for drug-protein binding leads to improved drug efficacy. Therefore, computational methods have been developed to predict kinetic rates and to derive quantitative structure-kinetic relationships (QSKRs). Many of these methods are based on crystal structures of ligand-protein complexes. However, a drawback is that each ligand-protein complex is usually treated as having a single structure. Here, we present a modification of COMparative BINding Energy (COMBINE) analysis, which uses the structures of ligand-protein complexes to predict binding parameters. We introduce the option of using multiple structures to describe each ligand-protein complex in COMBINE analysis and apply this to study the effects of protein flexibility on the derivation of dissociation rate constants (koff) for inhibitors of p38 mitogen-activated protein (MAP) kinase, which has a flexible binding site. Multiple structures were obtained for each ligand-protein complex by performing docking to an ensemble of protein configurations obtained from molecular dynamics simulations. Coefficients to scale ligand-protein interaction energies determined from energy-minimized structures of ligand-protein complexes were obtained by partial least squares regression, and they allowed for the computation of koff values. The QSKR model obtained using single, energy-minimized crystal structures for each ligand-protein complex had higher predictive power than the QSKR model obtained with multiple structures from ensemble docking. However, incorporation of ligand-protein flexibility helped to highlight additional ligand-protein interactions that lead to longer residence times, such as interactions with residues Arg67 and Asp168, which are close to the ligand in many crystal structures. These results show that COMBINE analysis is a promising method to guide the design of compounds that bind to flexible proteins with improved binding kinetics.
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Affiliation(s)
- Ariane Nunes-Alves
- Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Fabian Ormersbach
- Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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4
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Amangeldiuly N, Karlov D, Fedorov MV. Baseline Model for Predicting Protein–Ligand Unbinding Kinetics through Machine Learning. J Chem Inf Model 2020; 60:5946-5956. [DOI: 10.1021/acs.jcim.0c00450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nurlybek Amangeldiuly
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitry Karlov
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maxim V. Fedorov
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, Glasgow G4 0NG, U.K
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5
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Kokh DB, Kaufmann T, Kister B, Wade RC. Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times. Front Mol Biosci 2019; 6:36. [PMID: 31179286 PMCID: PMC6543870 DOI: 10.3389/fmolb.2019.00036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/02/2019] [Indexed: 12/25/2022] Open
Abstract
Drug-target residence times can impact drug efficacy and safety, and are therefore increasingly being considered during lead optimization. For this purpose, computational methods to predict residence times, τ, for drug-like compounds and to derive structure-kinetic relationships are desirable. A challenge for approaches based on molecular dynamics (MD) simulation is the fact that drug residence times are typically orders of magnitude longer than computationally feasible simulation times. Therefore, enhanced sampling methods are required. We recently reported one such approach: the τRAMD procedure for estimating relative residence times by performing a large number of random acceleration MD (RAMD) simulations in which ligand dissociation occurs in times of about a nanosecond due to the application of an additional randomly oriented force to the ligand. The length of the RAMD simulations is used to deduce τ. The RAMD simulations also provide information on ligand egress pathways and dissociation mechanisms. Here, we describe a machine learning approach to systematically analyze protein-ligand binding contacts in the RAMD trajectories in order to derive regression models for estimating τ and to decipher the molecular features leading to longer τ values. We demonstrate that the regression models built on the protein-ligand interaction fingerprints of the dissociation trajectories result in robust estimates of τ for a set of 94 drug-like inhibitors of heat shock protein 90 (HSP90), even for the compounds for which the length of the RAMD trajectories does not provide a good estimation of τ. Thus, we find that machine learning helps to overcome inaccuracies in the modeling of protein-ligand complexes due to incomplete sampling or force field deficiencies. Moreover, the approach facilitates the identification of features important for residence time. In particular, we observed that interactions of the ligand with the sidechain of F138, which is located on the border between the ATP binding pocket and a hydrophobic transient sub-pocket, play a key role in slowing compound dissociation. We expect that the combination of the τRAMD simulation procedure with machine learning analysis will be generally applicable as an aid to target-based lead optimization.
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Affiliation(s)
- Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Tom Kaufmann
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Department of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Bastian Kister
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Department of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Department of Physics, Heidelberg University, Heidelberg, Germany
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6
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Synthesis of 3-aminoindan-1-one derivatives from 2-acetylbenzaldehydes and secondary amines by Mannich annulation. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.04.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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7
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Fusani L, Cabrera AC. Active learning strategies with COMBINE analysis: new tricks for an old dog. J Comput Aided Mol Des 2019; 33:287-294. [PMID: 30564994 PMCID: PMC7087723 DOI: 10.1007/s10822-018-0181-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/14/2018] [Indexed: 11/09/2022]
Abstract
The COMBINE method was designed to study congeneric series of compounds including structural information of ligand-protein complexes. Although very successful, the method has not received the same level of attention than other alternatives to study Quantitative Structure Active Relationships (QSAR) mainly because lack of ways to measure the uncertainty of the predictions and the need for large datasets. Active learning, a semi-supervised learning approach that makes use of uncertainty to enhance models' performance while reducing the size of the training sets, has been used in this work to address both problems. We propose two estimators of uncertainty: the pool of regressors and the distance to the training set. The performance of the methods has been evaluated by testing the resulting active learning workflows in 3 diverse datasets: HIV-1 protease inhibitors, Taxol-derivatives and BRD4 inhibitors. The proposed strategies were successful in 80% of the cases for the taxol-derivatives and BRD4 inhibitors, while outperformed random selection in the case of the HIV-1 protease inhibitors time-split. Our results suggest that AL-COMBINE might be an effective way of producing consistently superior QSAR models with a limited number of samples.
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Affiliation(s)
- Lucia Fusani
- Molecular Design UK. GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Alvaro Cortes Cabrera
- Data Science and Computational Chemistry, Galchimia S.A. Severo Ochoa 2, Tres Cantos, 28760, Spain.
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8
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Ganotra GK, Wade RC. Prediction of Drug-Target Binding Kinetics by Comparative Binding Energy Analysis. ACS Med Chem Lett 2018; 9:1134-1139. [PMID: 30429958 PMCID: PMC6231175 DOI: 10.1021/acsmedchemlett.8b00397] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/04/2018] [Indexed: 12/02/2022] Open
Abstract
![]()
A growing
consensus is emerging that optimizing the drug–target
affinity alone under equilibrium conditions does not necessarily translate
into higher potency in vivo and that instead binding kinetic parameters
should be optimized to ensure better efficacy. Therefore, in silico
methods are needed to predict the kinetic parameters and the mechanistic
determinants of drug–protein binding. Here we demonstrate the
application of COMparative BINding Energy (COMBINE) analysis to derive
quantitative structure–kinetics relationships (QSKRs) for the
dissociation rate constants (koff) of
inhibitors of heat shock protein 90 (HSP90) and HIV-1 protease. We
derived protein-specific scoring functions by correlating koff rate constants with a subset of weighted
interaction energy components determined from the energy-minimized
structures of drug–protein complexes. As the QSKRs derived
for these sets of chemically diverse compounds have good predictive
ability and provide insights into important drug–protein interactions
for optimizing koff, COMBINE analysis
offers a promising approach for binding kinetics-guided lead optimization.
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Affiliation(s)
- Gaurav K. Ganotra
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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9
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Halder AK. Finding the structural requirements of diverse HIV-1 protease inhibitors using multiple QSAR modelling for lead identification. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:911-933. [PMID: 30332922 DOI: 10.1080/1062936x.2018.1529702] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/25/2018] [Indexed: 06/08/2023]
Abstract
Multiple Quantitative Structure-Activity Relationship (QSAR) analysis is widely used in drug discovery for lead identification. Human Immunodeficiency Virus (HIV) protease is one of the key targets for the treatment of Acquired Immunodeficiency Syndrome (AIDS). One of the major challenges for the design of HIV-1 protease inhibitors (HIV PRIs) is to increase the inhibitory activities against the enzyme to a level where the problem associated to drug resistance may be considerably delayed. Herein, chemometric analyses were performed with 346 structurally diverse HIV PRIs with experimental bioactivities against a sub-type B mutant to develop highly predictable QSAR models and also to identify the effective structural determinants for higher affinity against HIV PR. The QSAR models were developed using OCHEM-based machine learning tools (ASNN, FSMLR, KNN, RF, MANN and XGBoost), with descriptors calculated by eight different software packages. Simultaneously, a Monte Carlo optimization-based QSAR modelling was performed using SMILES and graph-based descriptors to understand fragment and topochemical contributions. To validate the actual predictability of all these models, an additional set of 104 compounds (also with known experimental activities) with slightly different chemical space were employed. This ligand-based study serves as a crucial benchmark for further development of the HIV protease inhibitors with improved activities.
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Affiliation(s)
- A K Halder
- a School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa
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10
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Liu L, Bai SH, Li Y, Wang LX, Hu Y, Sung HL, Li J. Synthesis of 2,3-Diarylisoindolin-1-one by Copper-Catalyzed Cascade Annulation of 2-Formylbenzonitriles, Arenes, and Diaryliodonium Salts. J Org Chem 2017; 82:11084-11090. [DOI: 10.1021/acs.joc.7b02035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | | | | | | | | | - Hui-Ling Sung
- Division
of Preparatory Programs for Overseas Chinese Students, National Taiwan Normal University, Linkou, 24449, Taiwan
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11
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Zhang T, Tian Y, Li Z, Liu S, Hu X, Yang Z, Ling X, Liu S, Zhang J. Molecular Dynamics Study to Investigate the Dimeric Structure of the Full-Length α-Synuclein in Aqueous Solution. J Chem Inf Model 2017; 57:2281-2293. [DOI: 10.1021/acs.jcim.7b00210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tingting Zhang
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Yuanxin Tian
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhonghuang Li
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Siming Liu
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Xiang Hu
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Zichao Yang
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Xiaotong Ling
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of
New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
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12
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Jia X, Guo Y, Lin X, You M, Lin C, Chen L, Chen J. Fusion of a family 20 carbohydrate-binding module (CBM20) with cyclodextrin glycosyltransferase of Geobacillus
sp. CHB1 improves catalytic efficiency. J Basic Microbiol 2017; 57:471-480. [DOI: 10.1002/jobm.201600628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/14/2017] [Accepted: 03/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Xianbo Jia
- Institute of Applied Ecology; Fujian Agriculture and Forestry University; Fuzhou China
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Yonghua Guo
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Xinjian Lin
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Minsheng You
- Institute of Applied Ecology; Fujian Agriculture and Forestry University; Fuzhou China
| | - Chenqiang Lin
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Longjun Chen
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Jichen Chen
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
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13
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Chaudhari TY, Ginotra SK, Tandon V. Facile access to functionalized indenes and fused quinolines by regioselective 5-enolexo-dig Michael addition and cyclization reactions. Org Biomol Chem 2017; 15:9319-9330. [DOI: 10.1039/c7ob02498c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report a facile approach to synthesise multi-substituted indenes and cyclopenta[b]quinolines under mild conditions.
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Affiliation(s)
| | | | - Vibha Tandon
- Special Centre for Molecular Medicine
- Jawaharlal Nehru University
- New Delhi-110067
- India
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14
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Teruya K, Hattori Y, Shimamoto Y, Kobayashi K, Sanjoh A, Nakagawa A, Yamashita E, Akaji K. Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold. Biopolymers 2016; 106:391-403. [PMID: 26572934 PMCID: PMC7159131 DOI: 10.1002/bip.22773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/22/2015] [Accepted: 11/02/2015] [Indexed: 02/03/2023]
Abstract
Design of inhibitors against severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro) ) is a potentially important approach to fight against SARS. We have developed several synthetic inhibitors by structure-based drug design. In this report, we reveal two crystal structures of SARS 3CL(pro) complexed with two new inhibitors based on our previous work. These structures combined with six crystal structures complexed with a series of related ligands reported by us are collectively analyzed. To these eight complexes, the structural basis for inhibitor binding was analyzed by the COMBINE method, which is a chemometrical analysis optimized for the protein-ligand complex. The analysis revealed that the first two latent variables gave a cumulative contribution ratio of r(2) = 0.971. Interestingly, scores using the second latent variables for each complex were strongly correlated with root mean square deviations (RMSDs) of side-chain heavy atoms of Met(49) from those of the intact crystal structure of SARS-3CL(pro) (r = 0.77) enlarging the S2 pocket. The substantial contribution of this side chain (∼10%) for the explanation of pIC50 s was dependent on stereochemistry and the chemical structure of the ligand adapted to the S2 pocket of the protease. Thus, starting from a substrate mimic inhibitor, a design for a central scaffold for a low molecular weight inhibitor was evaluated to develop a further potent inhibitor. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 391-403, 2016.
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Affiliation(s)
- Kenta Teruya
- Department of NeurochemistryTohoku University Graduate School of MedicineAoba‐Ku Sendai980‐8575Japan
| | - Yasunao Hattori
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | - Yasuhiro Shimamoto
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | - Kazuya Kobayashi
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | | | - Atsushi Nakagawa
- Institute for Protein Research, Osaka UniversitySuitaOsaka565‐0871Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka UniversitySuitaOsaka565‐0871Japan
| | - Kenichi Akaji
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
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15
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Cao Z, Zhu H, Meng X, Guan J, Zhang Q, Tian L, Sun X, Chen G, You J. Metal-Free Reaction ofortho-Carbonylated Alkynyl-Substituted Arylaldehydes with Common Amines: Selective Access to Functionalized Isoindolinone and Indenamine Derivatives. Chemistry 2016; 22:16979-16985. [DOI: 10.1002/chem.201603045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Ziping Cao
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Hongbo Zhu
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Xin Meng
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Jun Guan
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Qiang Zhang
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Laijin Tian
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Xuejun Sun
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Guang Chen
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Jinmao You
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
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16
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Kumar SP, George LB, Jasrai YT, Pandya HA. Prioritization of active antimalarials using structural interaction profile of Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR)-triclosan derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:61-77. [PMID: 25567142 DOI: 10.1080/1062936x.2014.984628] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An empirical relationship between the experimental inhibitory activities of triclosan derivatives and its computationally predicted Plasmodium falciparum enoyl-acyl carrier protein (ACP) reductase (PfENR) dock poses was developed to model activities of known antimalarials. A statistical model was developed using 57 triclosan derivatives with significant measures (r = 0.849, q(2) = 0.619, s = 0.481) and applied on structurally related and structurally diverse external datasets. A substructure-based search on ChEMBL malaria dataset (280 compounds) yielded only two molecules with significant docking energy, whereas eight active antimalarials (EC(50) < 100 nM, tested on 3D7 strain) with better predicted activities (pIC(50) ~ 7) from Open Access Malaria Box (400 compounds) were prioritized. Further, calculations on the structurally diverse rhodanine molecules (known PfENR inhibitors) distinguished actives (experimental IC(50) = 0.035 μM; predicted pIC(50) = 6.568) and inactives (experimental IC(50) = 50 μM; predicted pIC50 = -4.078), which showed that antimalarials possessing dock poses similar to experimental interaction profiles can be used as leads to test experimentally on enzyme assays.
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Affiliation(s)
- S P Kumar
- a Department of Bioinformatics, Applied Botany Centre (ABC) , University School of Sciences, Gujarat University , Ahmedabad , India
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17
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Khedkar VM, Joseph J, Pissurlenkar R, Saran A, Coutinho EC. How good are ensembles in improving QSAR models? The case with eCoRIA. J Biomol Struct Dyn 2014; 33:749-69. [DOI: 10.1080/07391102.2014.909744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Jose Joseph
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Raghuvir Pissurlenkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Anil Saran
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
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18
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Canales A, Nieto L, Rodríguez-Salarichs J, Sánchez-Murcia PA, Coderch C, Cortés-Cabrera A, Paterson I, Carlomagno T, Gago F, Andreu JM, Altmann KH, Jiménez-Barbero J, Díaz JF. Molecular recognition of epothilones by microtubules and tubulin dimers revealed by biochemical and NMR approaches. ACS Chem Biol 2014; 9:1033-43. [PMID: 24524625 DOI: 10.1021/cb400673h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The binding of epothilones to dimeric tubulin and to microtubules has been studied by means of biochemical and NMR techniques. We have determined the binding constants of epothilone A (EpoA) and B (EpoB) to dimeric tubulin, which are 4 orders of magnitude lower than those for microtubules, and we have elucidated the conformation and binding epitopes of EpoA and EpoB when bound to tubulin dimers and microtubules in solution. The determined conformation of epothilones when bound to dimeric tubulin is similar to that found by X-ray crystallographic techniques for the binding of EpoA to the Tubulin/RB3/TTL complex; it is markedly different from that reported for EpoA bound to zinc-induced sheets obtained by electron crystallography. Likewise, only the X-ray structure of EpoA bound to the Tubulin/RB3/TTL complex at the luminal site, but not the electron crystallography structure, is compatible with the results obtained by STD on the binding epitope of EpoA bound to dimeric tubulin, thus confirming that the allosteric change (structuring of the M-loop) is the biochemical mechanism of induction of tubulin assembly by epothilones. TR-NOESY signals of EpoA bound to microtubules have been obtained, supporting the interaction with a transient binding site with a fast exchange rate (pore site), consistent with the notion that epothilones access the luminal site through the pore site, as has also been observed for taxanes. Finally, the differences in the tubulin binding affinities of a series of epothilone analogues has been quantitatively explained using the newly determined binding pose and the COMBINE methodology.
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Affiliation(s)
- Angeles Canales
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Dep.
Química Orgánica I, Fac. C. Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, 28040 Madrid, Spain
| | - Lidia Nieto
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Javier Rodríguez-Salarichs
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro de
Estudios
Avanzados de Cuba, Carretera San Antonio
km 1 1/2, Valle Grande, La Lisa, Ciudad Habana CP 17100, Cuba
| | - Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Claire Coderch
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Alvaro Cortés-Cabrera
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Ian Paterson
- University
Chemical Laboratory, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Teresa Carlomagno
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - José M. Andreu
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Karl-Heinz Altmann
- Department
of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, HCI H405, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
| | - Jesús Jiménez-Barbero
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - J. Fernando Díaz
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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19
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Li J, Wei X, Tang C, Wang J, Zhao M, Pang Q, Wu M. Directed modification of the Aspergillus usamii β-mannanase to improve its substrate affinity by in silico design and site-directed mutagenesis. ACTA ACUST UNITED AC 2014; 41:693-700. [DOI: 10.1007/s10295-014-1406-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/16/2014] [Indexed: 01/30/2023]
Abstract
Abstract
β-Mannanases (EC 3.2.1.78) can catalyze the cleavage of internal β-1,4-d-mannosidic linkages of mannan backbones, and they have found applications in food, feed, pulp and paper, oil, pharmaceutical and textile industries. Suitable amino acid substitution can promote access to the substrate-binding groove and maintain the substrate therein, which probably improves the substrate affinity and, thus, increases catalytic efficiency of the enzyme. In this study, to improve the substrate affinity of AuMan5A, a glycoside hydrolase (GH) family 5 β-mannanase from Aspergillus usamii, had its directed modification conducted by in silico design, and followed by site-directed mutagenesis. The mutant genes, Auman5AY111F and Auman5AY115F, were constructed by megaprimer PCR, respectively. Then, Auman5A and its mutant genes were expressed in Pichia pastoris GS115 successfully. The specific activities of purified recombinant β-mannanases (reAuMan5A, reAuMan5AY111F and reAuMan5AY115F) towards locust bean gum were 152.5, 199.6 and 218.9 U mg−1, respectively. The two mutants were found to be similar to reAuMan5A regarding temperature and pH characteristics. Nevertheless, the K m values of reAuMan5AY111F and reAuMan5AY115F, towards guar gum, decreased to 2.95 ± 0.22 and 2.39 ± 0.33 mg ml−1 from 4.49 ± 0.07 mg ml−1 of reAuMan5A, which would make reAuMan5AY111F and reAuMan5AY115F promising candidates for industrial processes. Structural analysis showed that the two mutants increased their affinity by decreasing the steric conflicts with those more complicated substrates. The results suggested that subtle conformational modification in the substrate-binding groove could substantially alter the substrate affinity of AuMan5A. This study laid a solid foundation for the directed modification of substrate affinities of β-mannanases and other enzymes.
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Affiliation(s)
- Jianfang Li
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University 1800 Lihu Road 214122 Wuxi Jiangsu People’s Republic of China
| | - Xihuan Wei
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University 1800 Lihu Road 214122 Wuxi Jiangsu People’s Republic of China
| | - Cunduo Tang
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi Jiangsu People’s Republic of China
| | - Junqing Wang
- grid.258151.a 0000000107081323 School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi Jiangsu People’s Republic of China
| | - Mei Zhao
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University 1800 Lihu Road 214122 Wuxi Jiangsu People’s Republic of China
| | - Qingfeng Pang
- grid.258151.a 0000000107081323 Wuxi Medical School Jiangnan University 1800 Lihu Road 214122 Wuxi Jiangsu People’s Republic of China
| | - Minchen Wu
- grid.258151.a 0000000107081323 Wuxi Medical School Jiangnan University 1800 Lihu Road 214122 Wuxi Jiangsu People’s Republic of China
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20
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Krishna S, Singh DK, Meena S, Datta D, Siddiqi MI, Banerjee D. Pharmacophore-based screening and identification of novel human ligase I inhibitors with potential anticancer activity. J Chem Inf Model 2014; 54:781-92. [PMID: 24593844 DOI: 10.1021/ci5000032] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human DNA ligases are enzymes that are indispensable for DNA replication and repair processes. Among the three human ligases, ligase I is attributed to the ligation of thousands of Okazaki fragments that are formed during lagging strand synthesis during DNA replication. Blocking ligation therefore can lead to the accumulation of thousands of single strands and subsequently double strand breaks in the DNA, which is lethal for the cells. The reports of the high expression level of ligase I protein in several cancer cells (versus the low ligase expression level and the low rate of division of most normal cells in the adult body) support the belief that ligase I inhibitors can target cancer cells specifically with minimum side effects to normal cells. Recent publications showing exciting data for a ligase IV inhibitor exhibiting antitumor activity in mouse models also strengthens the argument for ligases as valid antitumor targets. Keeping this in view, we performed a pharmacophore-based screening for potential ligase inhibitors in the Maybridge small molecule library and procured some of the top-ranking compounds for enzyme-based and cell-based in vitro screening. We report here the identification of novel ligase I inhibitors with potential anticancer activity against a colon cancer cell line.
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Affiliation(s)
- Shagun Krishna
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute , Lucknow 226031, India
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21
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Coderch C, Tang Y, Klett J, Zhang SE, Ma YT, Shaorong W, Matesanz R, Pera B, Canales A, Jiménez-Barbero J, Morreale A, Díaz JF, Fang WS, Gago F. A structure-based design of new C2- and C13-substituted taxanes: tubulin binding affinities and extended quantitative structure-activity relationships using comparative binding energy (COMBINE) analysis. Org Biomol Chem 2013; 11:3046-56. [PMID: 23532250 DOI: 10.1039/c3ob40407b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ten novel taxanes bearing modifications at the C2 and C13 positions of the baccatin core have been synthesized and their binding affinities for mammalian tubulin have been experimentally measured. The design strategy was guided by (i) calculation of interaction energy maps with carbon, nitrogen and oxygen probes within the taxane-binding site of β-tubulin, and (ii) the prospective use of a structure-based QSAR (COMBINE) model derived from an earlier series comprising 47 congeneric taxanes. The tubulin-binding affinity displayed by one of the new compounds (CTX63) proved to be higher than that of docetaxel, and an updated COMBINE model provided a good correlation between the experimental binding free energies and a set of weighted residue-based ligand-receptor interaction energies for 54 out of the 57 compounds studied. The remaining three outliers from the original training series have in common a large unfavourable entropic contribution to the binding free energy that we attribute to taxane preorganization in aqueous solution in a conformation different from that compatible with tubulin binding. Support for this proposal was obtained from solution NMR experiments and molecular dynamics simulations in explicit water. Our results shed additional light on the determinants of tubulin-binding affinity for this important class of antitumour agents and pave the way for further rational structural modifications.
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Affiliation(s)
- Claire Coderch
- Área de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, E-28871 Alcalá de Henares, Unidad Asociada al Instituto de Química Médica del CSIC, Madrid, Spain
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22
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Kheffache D, Guemmour H, Dekhira A, Benaboura A, Ouamerali O. Conformational analysis and intramolecular hydrogen bonding of cis-3-aminoindan-1-ol: a quantum chemical study. J Mol Model 2013; 19:4837-47. [PMID: 24026578 DOI: 10.1007/s00894-013-1989-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 08/28/2013] [Indexed: 11/29/2022]
Abstract
In the present work, we carried out a conformational analysis of cis-3-aminoindan-1-ol and evaluated the role of the intramolecular hydrogen bond in the stabilization of various conformers using quantum mechanical DFT (B3LYP) and MP2 methods. On the basis of relative energies, we have found nine conformational minima, which can interchange through the ring-puckering and the internal rotation of the OH and NH2 groups on the five-membered ring. The intramolecular hydrogen bonds such as OH∙∙∙∙π, NH∙∙∙∙π, NH∙∙∙∙OH and HN∙∙∙∙HO are expected to be of critical importance for the conformational stabilities. The intramolecular interactions of the minima have been analyzed by calculation of electron density (ρ) and Laplacian (ρ) at the bond critical points (BCPs) using atoms-in-molecule (AIM) theory. The existence or absence of OH∙∙∙∙π and NH∙∙∙∙π in cis-3-aminoindan-1-ol remains unclear since the geometrical investigation has not been confirmed by topological criteria. The results of theoretical calculations demonstrate that this compound exists predominantly in one ring-puckering form stabilized by strong hydrogen bond HN∙∙∙∙HO Interaction.
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Affiliation(s)
- Djaffar Kheffache
- Laboratoire de Chimie Théorique Computationnelle et Photonique, Faculté de Chimie, Université des Sciences et de la Technologie Houari Boumediene USTHB, BP 32 El-alia, Bab ezzouar, Alger, 16111, Algeria,
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23
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Fusing a carbohydrate-binding module into the Aspergillus usamii β-mannanase to improve its thermostability and cellulose-binding capacity by in silico design. PLoS One 2013; 8:e64766. [PMID: 23741390 PMCID: PMC3669383 DOI: 10.1371/journal.pone.0064766] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/18/2013] [Indexed: 11/25/2022] Open
Abstract
The AuMan5A, an acidophilic glycoside hydrolase (GH) family 5 β-mannanase derived from Aspergillus usamii YL-01-78, consists of an only catalytic domain (CD). To perfect enzymatic properties of the AuMan5A, a family 1 carbohydrate-binding module (CBM) of the Trichoderma reesei cellobiohydrolase I (TrCBH I), having the lowest binding free energy with cellobiose, was selected by in silico design, and fused into its C-terminus forming a fusion β-mannanase, designated as AuMan5A-CBM. Then, its encoding gene, Auman5A-cbm, was constructed as it was designed theoretically, and expressed in Pichia pastoris GS115. SDS-PAGE analysis displayed that both recombinant AuMan5A-CBM (reAuMan5A-CBM) and AuMan5A (reAuMan5A) were secreted into the cultured media with apparent molecular masses of 57.3 and 49.8 kDa, respectively. The temperature optimum of the reAuMan5A-CBM was 75°C, being 5°C higher than that of the reAuMan5A. They were stable at temperatures of 68 and 60°C, respectively. Compared with reAuMan5A, the reAuMan5A-CBM showed an obvious decrease in Km and a slight alteration in Vmax. In addition, the fusion of a CBM of the TrCBH I into the AuMan5A contributed to its cellulose-binding capacity.
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24
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Fukunishi Y, Nakamura H. Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules. Pharmaceuticals (Basel) 2013; 6:604-22. [PMID: 24276169 PMCID: PMC3817721 DOI: 10.3390/ph6050604] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 11/16/2022] Open
Abstract
We previously developed the direct interaction approximation (DIA) method to estimate the protein-ligand binding free energy (DG). The DIA method estimates the DG value based on the direct van der Waals and electrostatic interaction energies between the protein and the ligand. In the current study, the effect of the entropy of the ligand was introduced with protein dynamic properties by molecular dynamics simulations, and the interaction between each residue of the protein and the ligand was also weighted considering the hydration of each residue. The molecular dynamics simulation of the apo target protein gave the hydration effect of each residue, under the assumption that the residues, which strongly bind the water molecules, are important in the protein-ligand binding. These two effects improved the reliability of the DIA method. In fact, the parameters used in the DIA became independent of the target protein. The averaged error of DG estimation was 1.3 kcal/mol and the correlation coefficient between the experimental DG value and the calculated DG value was 0.75.
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Affiliation(s)
- Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-3-3599-8290; Fax: +81-3-3599-8099
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail:
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25
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Peón A, Coderch C, Gago F, González-Bello C. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors. ChemMedChem 2013; 8:740-7. [PMID: 23450741 DOI: 10.1002/cmdc.201300013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Indexed: 11/08/2022]
Abstract
Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.
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Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biológica y Materiales, Moleculares CIQUS, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela Spain
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26
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Limiting assumptions in molecular modeling: electrostatics. J Comput Aided Mol Des 2013; 27:107-14. [PMID: 23354627 DOI: 10.1007/s10822-013-9634-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Abstract
Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.
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27
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Chen X, Hu XY, Shu C, Zhang YH, Zheng YS, Jiang Y, Yuan WC, Liu B, Zhang XM. Synthesis of a series of novel chiral Lewis base catalysts and their application in promoting asymmetric hydrosilylation of β-enamino esters. Org Biomol Chem 2013; 11:3089-93. [PMID: 23563603 DOI: 10.1039/c3ob40430g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Xing Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610041 China
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28
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Qian H, Zhao W, Sung HHY, Williams ID, Sun J. Stereoselective synthesis of aminoindanols via an efficient cascade aza-Michael–aldol reaction. Chem Commun (Camb) 2013; 49:4361-3. [DOI: 10.1039/c2cc37102b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Molecular simulations of drug–receptor complexes in anticancer research. Future Med Chem 2012; 4:1961-70. [DOI: 10.4155/fmc.12.149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Molecular modeling and computer simulation techniques have matured significantly in recent years and proved their value in the study of drug–DNA, drug–DNA–protein, drug–protein and protein–protein interactions. Evolution in this area has gone hand-in-hand with an increased availability of structural data on biological macromolecules, major advances in molecular mechanics force fields and considerable improvements in computer technologies, most significantly processing speeds, multiprocessor programming and data-storage capacity. The information derived from molecular simulations of drug–receptor complexes can be used to extract structural and energetic information that is usually beyond current experimental possibilities, provide independent accounts of experimentally observed behavior, help in the interpretation of biochemical or pharmacological results, and open new avenues for research by posing novel relevant questions that can guide the design of new experiments. As drug-screening tools, ligand- and fragment-docking platforms stand out as powerful techniques that can provide candidate molecules for hit and lead development. This review provides an overall perspective of the main methods and focuses on some selected applications to both classical and novel anticancer targets.
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30
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Fukunishi Y, Nakamura H. Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation. Pharmaceuticals (Basel) 2012; 5:1064-79. [PMID: 24281257 PMCID: PMC3816655 DOI: 10.3390/ph5101064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 11/28/2022] Open
Abstract
We have developed a method for estimating protein-ligand binding free energy (DG) based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the DG value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA) and dihedral angles of the protein-ligand complex system as the entropy terms of the DG estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated DG values was 0.81, and the average error of DG was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan;
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Liu S, Fu R, Cheng X, Chen SP, Zhou LH. Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE). BMC STRUCTURAL BIOLOGY 2012; 12:21. [PMID: 22925713 PMCID: PMC3533579 DOI: 10.1186/1472-6807-12-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 08/03/2012] [Indexed: 01/14/2023]
Abstract
BACKGROUND The inhibition of the activity of β-secretase (BACE-1) is a potentially important approach for the treatment of Alzheimer disease. To explore the mechanism of inhibition, we describe the use of 46 X-ray crystallographic BACE-1/inhibitor complexes to derive quantitative structure-activity relationship (QSAR) models. The inhibitors were aligned by superimposing 46 X-ray crystallographic BACE-1/inhibitor complexes, and gCOMBINE software was used to perform COMparative BINding Energy (COMBINE) analysis on these 46 minimized BACE-1/inhibitor complexes. The major advantage of the COMBINE analysis is that it can quantitatively extract key residues involved in binding the ligand and identify the nature of the interactions between the ligand and receptor. RESULTS By considering the contributions of the protein residues to the electrostatic and van der Waals intermolecular interaction energies, two predictive and robust COMBINE models were developed: (i) the 3-PC distance-dependent dielectric constant model (built from a single X-ray crystal structure) with a q2 value of 0.74 and an SDEC value of 0.521; and (ii) the 5-PC sigmoidal electrostatic model (built from the actual complexes present in the Brookhaven Protein Data Bank) with a q2 value of 0.79 and an SDEC value of 0.41. CONCLUSIONS These QSAR models and the information describing the inhibition provide useful insights into the design of novel inhibitors via the optimization of the interactions between ligands and those key residues of BACE-1.
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Affiliation(s)
- Shu Liu
- Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Rao Fu
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Xiao Cheng
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Sheng-Ping Chen
- Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Li-Hua Zhou
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
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Ballante F, Musmuca I, Marshall GR, Ragno R. Comprehensive model of wild-type and mutant HIV-1 reverse transciptases. J Comput Aided Mol Des 2012; 26:907-19. [DOI: 10.1007/s10822-012-9586-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
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Silvestri L, Ballante F, Mai A, Marshall GR, Ragno R. Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction. J Chem Inf Model 2012; 52:2215-35. [DOI: 10.1021/ci300160y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Laura Silvestri
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Flavio Ballante
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Antonello Mai
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Garland R. Marshall
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Rino Ragno
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
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Zhu X, Bora RP, Barman A, Singh R, Prabhakar R. Dimerization of the Full-Length Alzheimer Amyloid β-Peptide (Aβ42) in Explicit Aqueous Solution: A Molecular Dynamics Study. J Phys Chem B 2012; 116:4405-16. [DOI: 10.1021/jp210019h] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
| | - Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
| | - Rajiv Singh
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
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Coderch C, Klett J, Morreale A, Díaz JF, Gago F. Comparative Binding Energy (COMBINE) Analysis Supports a Proposal for the Binding Mode of Epothilones to β-Tubulin. ChemMedChem 2012; 7:836-43. [DOI: 10.1002/cmdc.201200065] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/02/2012] [Indexed: 01/08/2023]
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Zhang S. Application of Machine Leaning in Drug Discovery and Development. Mach Learn 2012. [DOI: 10.4018/978-1-60960-818-7.ch517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Machine learning techniques have been widely used in drug discovery and development, particularly in the areas of cheminformatics, bioinformatics and other types of pharmaceutical research. It has been demonstrated they are suitable for large high dimensional data, and the models built with these methods can be used for robust external predictions. However, various problems and challenges still exist, and new approaches are in great need. In this Chapter, the authors will review the current development of machine learning techniques, and especially focus on several machine learning techniques they developed as well as their application to model building, lead discovery via virtual screening, integration with molecular docking, and prediction of off-target properties. The authors will suggest some potential different avenues to unify different disciplines, such as cheminformatics, bioinformatics and systems biology, for the purpose of developing integrated in silico drug discovery and development approaches.
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Affiliation(s)
- Shuxing Zhang
- The University of Texas at M.D. Anderson Cancer Center, USA
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37
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Sotriffer C, Matter H. The Challenge of Affinity Prediction: Scoring Functions for Structure-Based Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Abia D, Bastolla U, Chacón P, Fábrega C, Gago F, Morreale A, Tramontano A. In memoriam. Proteins 2010; 78:iii-viii. [DOI: 10.1002/prot.22660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Comparative binding energy analysis for binding affinity and target selectivity prediction. Proteins 2009; 78:135-53. [DOI: 10.1002/prot.22579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Gil-Redondo R, Klett J, Gago F, Morreale A. gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes. Proteins 2009; 78:162-72. [DOI: 10.1002/prot.22543] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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41
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Kuzmanovski I, Novič M, Trpkovska M. Automatic adjustment of the relative importance of different input variables for optimization of counter-propagation artificial neural networks. Anal Chim Acta 2009; 642:142-7. [DOI: 10.1016/j.aca.2009.01.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 11/25/2008] [Accepted: 01/19/2009] [Indexed: 10/21/2022]
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42
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Priego EM, Pérez-Pérez MJ, von Frijtag Drabbe Kuenzel JK, de Vries H, Ijzerman AP, Camarasa MJ, Martín-Santamaría S. Selective human adenosine A3 antagonists based on pyrido[2,1-f]purine-2,4-diones: novel features of hA3 antagonist binding. ChemMedChem 2008; 3:111-9. [PMID: 18000937 DOI: 10.1002/cmdc.200700173] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Based on our previous results on the potent antagonist effect of 1H,3H-pyrido[2,1-f]purine-2,4-diones at the human A(3) adenosine receptor, new series of this family of compounds have been synthesized and evaluated in radioligand binding studies against the human A(1), A(2A), A(2B), and A(3) receptors. A remarkable improvement in potency, and most noticeable, in selectivity has been achieved, as exemplified by the 3-cyclopropylmethyl-8-methoxy-1-(4-methylbenzyl)-1H,3H-pyrido[2,1-f]purine-2,4-dione (10) that combines a very high affinity at hA(3) (K(i)=2.24 nM), with lack of affinity for the A(1), A(2A), and A(2B) receptors. On the basis of the published hA(3) receptor model (PDB 1OEA), molecular modeling studies, including molecular dynamics (MD) simulations, have been performed to depict the binding mode of the 1 H,3H-pyrido[2,1-f]purine-2,4-diones and to justify the selectivity against the other adenosine receptors. These studies have led to novel features of the cavity where our antagonists are bound so that the cavity is lined by the hydrogen-bonded Gln 167-Asn 250 pair and by the highly conserved Phe 168.
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Affiliation(s)
- Eva-María Priego
- Instituto de Química Médica, C.S.I.C. Juan de la Cierva 3, E-28006 Madrid, Spain
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Docking and multivariate methods to explore HIV-1 drug-resistance: a comparative analysis. J Comput Aided Mol Des 2008; 22:287-97. [PMID: 18273557 DOI: 10.1007/s10822-008-9186-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 01/23/2008] [Indexed: 10/22/2022]
Abstract
In this paper we describe a comparative analysis between multivariate and docking methods in the study of the drug resistance to the reverse transcriptase and the protease inhibitors. In our early papers we developed a simple but efficient method to evaluate the features of compounds that are less likely to trigger resistance or are effective against mutant HIV strains, using the multivariate statistical procedures PCA and DA. In the attempt to create a more solid background for the prediction of susceptibility or resistance, we carried out a comparative analysis between our previous multivariate approach and molecular docking study. The intent of this paper is not only to find further support to the results obtained by the combined use of PCA and DA, but also to evidence the structural features, in terms of molecular descriptors, similarity, and energetic contributions, derived from docking, which can account for the arising of drug-resistance against mutant strains.
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44
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Negri A, Marco E, García-Hernández V, Domingo A, Llamas-Saiz AL, Porto-Sandá S, Riguera R, Laine W, David-Cordonnier MH, Bailly C, García-Fernández LF, Vaquero JJ, Gago F. Antitumor Activity, X-ray Crystal Structure, and DNA Binding Properties of Thiocoraline A, a Natural Bisintercalating Thiodepsipeptide. J Med Chem 2007; 50:3322-33. [PMID: 17571868 DOI: 10.1021/jm070381s] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine natural product thiocoraline A displayed approximately equal cytotoxic activity at nanomolar concentrations in a panel of 12 human cancer cell lines. X-ray diffraction analyses of orthorhombic crystals of this DNA-binding drug revealed arrays of docked pairs of staple-shaped molecules in which one pendent hydroxyquinoline chromophore from each cysteine-rich molecule appears intercalated between the two chromophores of a facing molecule. This arrangement is in contrast to the proposed mode of binding to DNA that shows the two drug chromophores clamping two stacked base pairs, in agreement with the nearest-neighbor exclusion principle. Proof of DNA sequence recognition was obtained from both classical DNase I footprinting experiments and determination of the melting temperatures of several custom-designed fluorescently labeled oligonucleotides. A rationale for the DNA-binding behavior was gained when models of thiocoraline clamping a central step embedded in several octanucleotides were built and studied by means of unrestrained molecular dynamics simulations in aqueous solution.
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Affiliation(s)
- Ana Negri
- Departamento de Farmacología, Universidad de AlcalA, E-28871 Madrid, Spain
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45
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Grosdidier A, Zoete V, Michielin O. EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins 2007; 67:1010-25. [PMID: 17380512 DOI: 10.1002/prot.21367] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In recent years, protein-ligand docking has become a powerful tool for drug development. Although several approaches suitable for high throughput screening are available, there is a need for methods able to identify binding modes with high accuracy. This accuracy is essential to reliably compute the binding free energy of the ligand. Such methods are needed when the binding mode of lead compounds is not determined experimentally but is needed for structure-based lead optimization. We present here a new docking software, called EADock, that aims at this goal. It uses an hybrid evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with the CHARMM package for energy calculations and coordinate handling. A validation was carried out on 37 crystallized protein-ligand complexes featuring 11 different proteins. The search space was defined as a sphere of 15 A around the center of mass of the ligand position in the crystal structure, and on the contrary to other benchmarks, our algorithm was fed with optimized ligand positions up to 10 A root mean square deviation (RMSD) from the crystal structure, excluding the latter. This validation illustrates the efficiency of our sampling strategy, as correct binding modes, defined by a RMSD to the crystal structure lower than 2 A, were identified and ranked first for 68% of the complexes. The success rate increases to 78% when considering the five best ranked clusters, and 92% when all clusters present in the last generation are taken into account. Most failures could be explained by the presence of crystal contacts in the experimental structure. Finally, the ability of EADock to accurately predict binding modes on a real application was illustrated by the successful docking of the RGD cyclic pentapeptide on the alphaVbeta3 integrin, starting far away from the binding pocket.
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Affiliation(s)
- Aurélien Grosdidier
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Quartier Sorges, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
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46
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Tomić S, Bertosa B, Wang T, Wade RC. COMBINE analysis of the specificity of binding of Ras proteins to their effectors. Proteins 2007; 67:435-47. [PMID: 17295314 DOI: 10.1002/prot.21321] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The small guanosine triphosphate (GTP)-binding proteins of the Ras family are involved in many cellular pathways leading to cell growth, differentiation, and apoptosis. Understanding the interaction of Ras with other proteins is of importance not only for studying signalling mechanisms but also, because of their medical relevance as targets, for anticancer therapy. To study their selectivity and specificity, which are essential to their signal transfer function, we performed COMparative BINding Energy (COMBINE) analysis for 122 different wild-type and mutant complexes between the Ras proteins, Ras and Rap, and their effectors, Raf and RalGDS. The COMBINE models highlighted the amino acid residues responsible for subtle differences in binding of the same effector to the two different Ras proteins, as well as more significant differences in the binding of the two different effectors (RalGDS and Raf) to Ras. The study revealed that E37, D38, and D57 in Ras are nonspecific hot spots at its effector interface, important for stabilization of both the RalGDS-Ras and Raf-Ras complexes. The electrostatic interaction between a GTP analogue and the effector, either Raf or RalGDS, also stabilizes these complexes. The Raf-Ras complexes are specifically stabilized by S39, Y40, and D54, and RalGDS-Ras complexes by E31 and D33. Binding of a small molecule in the vicinity of one of these groups of amino acid residues could increase discrimination between the Raf-Ras and RalGDS-Ras complexes. Despite the different size of the RalGDS-Ras and Raf-Ras complexes, we succeeded in building COMBINE models for one type of complex that were also predictive for the other type of protein complex. Further, using system-specific models trained with only five complexes selected according to the results of principal component analysis, we were able to predict binding affinities for the other mutants of the particular Ras-effector complex. As the COMBINE analysis method is able to explicitly reveal the amino acid residues that have most influence on binding affinity, it is a valuable aid for protein design.
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47
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Gohda K. A quantitative structure-activity relationship study for structurally diverse HIV-1 protease inhibitors: Contribution of conformational flexibility to inhibitory activity. J Enzyme Inhib Med Chem 2006; 21:609-15. [PMID: 17194035 DOI: 10.1080/14756360600810233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
In this study, we investigated by linear regression model the SAR data of the 15 HIV-1 protease inhibitors possessing structurally diverse scaffolds. First, a regression model was developed only using the enzyme-inhibitor interaction energy as a term of the model, but did not provide a good correlation with the inhibitory activity (R2 = 0.580 and Q2 = 0.500). Then, we focused on the conformational flexibility of the inhibitors which may represent the diversity of the inhibitors, and added two conformational parameters into the model, respectively: the number of rotatable bonds of ligands (deltaSrot) and the distortion energy of ligands (deltaElig). The regression model by adding deltaElig successfully improved the quality of the model (R2 = 0.771 and Q2 = 0.713) while the model with deltaSrot was unsuccessful. The prediction for a training inhibitor by the deltaElig model also showed good agreement with experimental activity. These results suggest that the conformational flexibility of HIV-1 protease inhibitors directly contributes to the enzyme inhibition.
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Affiliation(s)
- Keigo Gohda
- Computer-Aided Molecular Modeling Research Center Kansai (CAMM Kansai), 2-8-20-404, Mikagehonmachi, Higashinada-ku Kobe 658-0046, Japan.
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48
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Zhang S, Golbraikh A, Oloff S, Kohn H, Tropsha A. A novel automated lazy learning QSAR (ALL-QSAR) approach: method development, applications, and virtual screening of chemical databases using validated ALL-QSAR models. J Chem Inf Model 2006; 46:1984-95. [PMID: 16995729 PMCID: PMC2536695 DOI: 10.1021/ci060132x] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel automated lazy learning quantitative structure-activity relationship (ALL-QSAR) modeling approach has been developed on the basis of the lazy learning theory. The activity of a test compound is predicted from a locally weighted linear regression model using chemical descriptors and the biological activity of the training set compounds most chemically similar to this test compound. The weights with which training set compounds are included in the regression depend on the similarity of those compounds to a test compound. We have applied the ALL-QSAR method to several experimental chemical data sets including 48 anticonvulsant agents with known ED50 values, 48 dopamine D1-receptor antagonists with known competitive binding affinities (Ki), and a Tetrahymena pyriformis data set containing 250 phenolic compounds with toxicity IGC50 values. When applied to database screening, models developed for anticonvulsant agents identified several known anticonvulsant compounds that were not only absent in the training set but highly chemically dissimilar to the training set compounds. This initial success indicates that ALL-QSAR can be further exploited as a general tool for accurate bioactivity prediction and database screening in drug design and discovery. Because of its local nature, the ALL-QSAR approach appears to be especially well-suited for the development of highly predictive models for the sparse or unevenly distributed data sets.
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Affiliation(s)
| | | | | | | | - Alexander Tropsha
- Corresponding author, School of Pharmacy, Campus Box 7360, 327 Beard Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360., Telephone (919) 966-2955, FAX: (919) 966-0204,
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49
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Wu YJ. Michael addition of 3-bromoinden-1-one: an expedient synthesis of 5-bromo-3-trifluoroacetamidoindan-1-one. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.09.151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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50
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Nakamura S, Nakanishi I, Kitaura K. Binding affinity prediction of non-peptide inhibitors of HIV-1 protease using COMBINE model introduced from peptide inhibitors. Bioorg Med Chem Lett 2006; 16:6334-7. [PMID: 17027266 DOI: 10.1016/j.bmcl.2006.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 09/01/2006] [Accepted: 09/05/2006] [Indexed: 11/17/2022]
Abstract
Comparative binding energy (COMBINE) analysis method is one of the QSAR techniques for the prediction of biological activities of inhibitors based on interaction energies between ligands and proteins decomposed into each amino acid residue. We supposed that the predictive ability of the COMBINE method does not depend essentially on the molecular frameworks of ligands. To verify this idea, we performed the COMBINE analysis of non-peptide inhibitors of HIV-1 protease (HIVp), where the prediction model was constructed using inhibitors with a peptide scaffold as a training set. The predictive performance of the AMBER and CHARMm force fields was very high and at the same level (q(2)=0.75, 0.67, SDEP(cv)=0.76, 0.89, and SDEP(ex)=0.92, 0.66, respectively). The high predictive ability of the COMBINE method for the distinct scaffold compounds is due to the informative description of the interaction energies for compounds that are located at the binding site. This result suggests that COMBINE analysis may be applied not only to the lead optimization stage but also to the lead evolution stages.
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Affiliation(s)
- Shinya Nakamura
- Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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